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- PDB-1g8q: CRYSTAL STRUCTURE OF HUMAN CD81 EXTRACELLULAR DOMAIN, A RECEPTOR ... -

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Basic information

Entry
Database: PDB / ID: 1g8q
TitleCRYSTAL STRUCTURE OF HUMAN CD81 EXTRACELLULAR DOMAIN, A RECEPTOR FOR HEPATITIS C VIRUS
ComponentsCD81 ANTIGEN, EXTRACELLULAR DOMAIN
KeywordsIMMUNE SYSTEM / Alpha Helical
Function / homology
Function and homology information


positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion ...positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion / transferrin receptor binding / immunological synapse formation / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / tetraspanin-enriched microdomain / positive regulation of protein exit from endoplasmic reticulum / MHC class II protein binding / humoral immune response mediated by circulating immunoglobulin / positive regulation of CD4-positive, alpha-beta T cell proliferation / cholesterol binding / positive regulation of T cell receptor signaling pathway / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of B cell proliferation / positive regulation of receptor clustering / basal plasma membrane / Regulation of Complement cascade / protein localization to plasma membrane / regulation of protein stability / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / MHC class II protein complex binding / virus receptor activity / basolateral plasma membrane / vesicle / positive regulation of MAPK cascade / focal adhesion / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsKitadokoro, K. / Bolognesi, M. / Bordo, D. / Grandi, G. / Galli, G. / Petracca, R. / Falugi, F.
CitationJournal: EMBO J. / Year: 2001
Title: CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs.
Authors: Kitadokoro, K. / Bordo, D. / Galli, G. / Petracca, R. / Falugi, F. / Abrignani, S. / Grandi, G. / Bolognesi, M.
History
DepositionNov 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD81 ANTIGEN, EXTRACELLULAR DOMAIN
B: CD81 ANTIGEN, EXTRACELLULAR DOMAIN


Theoretical massNumber of molelcules
Total (without water)19,8342
Polymers19,8342
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-17 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.485, 77.172, 38.462
Angle α, β, γ (deg.)90.00, 107.39, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein CD81 ANTIGEN, EXTRACELLULAR DOMAIN / CD81 / TARGET OF ANTIPROLIFERATIVE ANTIBODY 1 / 26 KDA CELL SURFACE PROTEIN TAPA-1


Mass: 9917.077 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PEZZ18 / Production host: Escherichia coli (E. coli) / References: UniProt: P60033
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 4000, MES, NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
215 %(w/v)PEG40001reservoir
30.1 M1reservoirNaCl
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 1999
RadiationMonochromator: Sagitally focusing Ge(220) and a multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 36910 / Num. obs: 21557 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 5.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.303 / Num. unique all: 2249 / Rsym value: 0.314 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 93.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1104 4.8 %RANDOM
Rwork0.188 ---
all-36910 --
obs-23143 93 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 0 194 1550
Refine LS restraintsType: refmac / Dev ideal: 0.022
LS refinement shellResolution: 1.6→1.673 Å / Rfactor Rfree error: 0.082
RfactorNum. reflection% reflection
Rfree0.373 116 -
Rwork0.291 --
obs-2625 85.2 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.2

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